Abstract Most studies of the microbiota and its role in inflammatory diseases in the intestines have focused on bacteria. However, eukaryotes and viruses are also present and are likely to exert an impact on health and disease in the gut. In previous studies, we have documented the complexity of the fungal community in the intestines of mice and observed that effective host immunity to fungi is important in controlling inflammation in colitis models. In preliminary data provided in this proposal, and conducted in collaboration with other members of this program project grant (PPG), we document the complexity of the colonic mucosa-associated fungal community in humans and observe significant differences in fungal communities found in patients with Crohn's Disease (CD). The overall hypothesis of this proposal is that fungal communities in the gut affect and are affected by the immune system and that these processes contribute to Crohn's disease. In the first Aim, we will characterize in vitro immune responses to two fungi that are strongly associated with CD. We will investigate the roles of Dectin-1 and CARD9 (two proteins in which genetic polymorphisms have been linked to CD and/or Ulcerative Colitis) in immune sensing of these fungi. In the second Aim, we will investigate the effects of these fungi on the makeup of the intestinal microbiome in mice, and determine the effects of these fungi on the severity of disease in mouse models of colitis. In the third Aim, we will further define the presence of these fungi in healthy people and in patients with CD, and in collaboration with other PPG members we will identify associations between fungi and bacteria, metabolites, serology, and host genetics.